fixed issue 46

walaj · Jun 1, 2019 · 0877128 · 0877128
1 parent 7e1f982
commit 0877128
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/SeqLib/BamRecord.h b/SeqLib/BamRecord.h
@@ -639,9 +639,9 @@ class BamRecord {
     uint32_t* c = bam_get_cigar(b);
     int32_t p = 0;
     for (size_t i = 0; i < b->core.n_cigar; ++i) {
-      if ( (bam_cigar_opchr(c[i]) == 'S') || (bam_cigar_opchr(c[i]) == 'H'))
+      if (bam_cigar_opchr(c[i]) == 'S')
 	p += bam_cigar_oplen(c[i]);
-      else // not a clip, so stop counting
+      else if (bam_cigar_opchr(c[i]) != 'H') 
 	break;
     }
     return p;